The purpose of this study was to quantify the effect of neck contour changes and setup errors on spinal cord (SC) doses during the treatment of nasopharyngeal carcinoma (NPC) and to establish a rapid dose estimation method. The setup errors and contour changes in 60 cone-beam computed tomography (CBCT) images of 10 NPC patients were analysed in different regions of the neck (C1–C3, C4–C5 and C6–C7). The actual delivered dose to the SC was calculated using the CBCT images, and univariate simulations were performed using the planning CT to evaluate the dose effects of each factor, and an index n}{}{mathrm{Dmax}}_{mathrm{displaced}} was introduced to estimate the SC dose. Compared with the planned dose, the mean (maximum) Dmax increases in the C1–C3, C4–C5 and C6–C7 regions of the SC were 2.1% (12.3%), 1.8% (8.2%) and 2.5% (9.2%), respectively. The simulation results showed that the effects of setup error in the C1–C3, C4–C5 and C6–C7 regions were 1.5% (9.7%), 0.9% (8.2%) and 1.3% (6.3%), respectively, and the effects of contour change were 0.4% (1.7%), 0.7% (2.5%) and 1.5% (4.9%), respectively. The linear regression model can be used to estimate the dose effect of contour changes (R2 > 0.975) and setup errors (R2 = 0.989). Setup errors may lead to a significant increase in the SC dose in some patients. This study established a rapid dose estimation method, which is of great significance for the daily dose evaluation and the adaptive re-planning trigger of the SC.